Incomplete messages when I'm running Pipeline

[ekan]

I'm running a pipeline that has run through completely before for many projects. I've verified that my input files are not bad or corrupted.

When I run the pipeline I get the following error from the first module, which happens to be a smartline:

/usr/local/smartline/runSmartLine.sh: line 60: cd: /usr/local/smartline: Not a directory
Could not create the Java virtual machine.

I've run the pipeline over the same files multiple times, and each time a different subject has this error. Sometimes it is only 1 subject, sometimes it's half my subjects....

Any ideas?
Thanks,
Eric

[zliu]

Hi Eric,

Sounds like problem with the compute node. Can you give me the host name? It's at the top of output stream called "SGE Exechost".

Thanks,
Zhizhong

[ekan]

Here you go from my last run of 24:

For several that failed (not sure if this will be all the nodes affected):
SGE Exechost: cerebro-5-114.data.cluster.loni.ucla.edu
SGE Exechost: cerebro-5-134.data.cluster.loni.ucla.edu
SGE Exechost: cerebro-8-133.data.cluster.loni.ucla.edu
SGE Exechost: cerebro-7-113.data.cluster.loni.ucla.edu

Thanks,
Eric

[zliu]

Hi Eric,

Some of the compute nodes were not functioning properly. System admins disabled these nodes for now. Please let us know if you have any problems.

Thanks,
Zhizhong

[ekan]

Thanks,

Disabling the problematic nodes have fixed the issue.